The Sun says Blackburn now rate the player at closer to £25million, rather than the £16.5m United expect to end up paying.
United remain confident they still have their man, after the 19-year-old defender agreed personal terms and passed a medical on Wednesday.
But they are growing increasingly frustrated by Rovers' reluctance to OK the switch.
United agreed to meet the £16m buy-out clause inserted in the new five-year contract Jones signed in February.
But now Rovers' owners Venky's are indicating it does not force them to accept any such bid and they value Jones at around that £25m figure.
The legal issue has not been ironed out in three days but Old Trafford sources still expect the deal to go through.